Normal maturation of immune response at birth is both supported and stimulated by the gastrointestinal microenvironment, which provides both nutrients and antigenic microbial exposure to the developing child. Micronutrients, trace elements, and vitamins are present in the local environment and have important regulatory effects on adaptive immune cell function through effects on type of cytokine response. Congenital HIV infection is critically affected by both nutrient imbalance and alteration in gastrointestinal microflora, which may impair growth and development as well as immune response. Studies described here indicate that micronutrient deficiency is common in congenital HIV exposure even where infection has not occurred and that gastrointestinal recolonization may exert a restorative effect on both immune response and growth in children with HIV infection.